Aquaveo & Water Resources Engineering News

Problem Solving and the Fix Layer Errors Tool

When creating multilayer models, defining layer data can be challenging. This is true for cases involving embedded seams, pinchouts, and truncations. Fortunately, Ground-water Modeling System (GMS) contains a suite of tools for interpolating and manipulating layer elevation data. With the tools in GMS), even complex geologic strata can be modeled quickly and easily. When interpolating layer data for the purpose of defining MODFLOW layer elevation arrays, there are often cases where the interpolated values overlap. In some cases, the best way to fix such a problem is to experiment with the interpolation options or to create some "pseudo-points" to fill in the gaps between sparse scatter points. In other cases, the overlap may correspond to a pinchout or truncation in the layer. In such cases, the elevations need to be adjusted so that there is a small but finite thickness for all cells in the overlapping region.

The first step in fixing layer errors is to use the Model Checker to determine if elevation overlaps occur. If they do occur, the Fix Layer Errors button at the top of the Model Checker dialog can be used to bring up the Fix Layer Errors dialog. Four options are available for fixing layer errors, including Average, Preserve Top, Preserve Bottom, and Truncate to Bedrock. The Average method is useful for modeling the transition zones adjacent to embedded seams. The Preserve Top method can be used to model truncated outcroppings. With the Preserve bottom method, at each cell where an overlap is found the bottom elevation is unchanged and the top elevation is adjusted to top = bot + min thickness. The Truncate to bedrock option differs from the other methods in that it can be used to alter several layers at once.

These are hypothetical scenarios that outline problems and solutions you may encounter when using the Fix Layer Errors Tool in GMS:

Fix Layer Errors Example

You are trying to construct a UGrid model that includes refinement around streams and pumping wells with refinement reserved for the top layers, and inactive cells with a thickness of less than 10 cm.

  1. You want a UGrid that includes refinement around streams and pumping wells, yet reserved for the top layers. You get the impression that reserved refinement is achievable only by using the preserve top method.
    It is correct that the preserve top method is a way to apply refinement. The average method does not have any way to refine certain areas, unless the 2D geometry being used as the base already has that refinement. In that case, the refinement would be added to all layers. In other words, refine the 2D grid first, but use the TIN method to create the grid based on that refinement. Use your judgment on if method one works better for your elevation data.
  2. You would like all cells with a thickness of less than 10 cm to be inactivated. Yet you find that the only way to inactivate cells less than 10 cm is by using the average method.
    Using the average method and setting the minimum thickness to 0.1m ≠ inactive thin cells. It means cells less than the minimum thickness are not created. Cells are not inactivated until after a MODFLOW simulation has been added. As such, they cannot be inactivated during the creation process. If this is not the result, and there does appear to be thin cells for a TIN grid, further action would be required.

Access the latest version of GMS 10.8 to make use of the Fix Layer Errors tool today!

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Tips for Pressure Zones with Overtopping in SRH-2D Models

Does your SRH-2D project have a box culvert or pressure zone with overtopping that is proving to be a bit difficult to get correct?

Box culverts or pressure zones with overtopping are common features added to many SRH-2D models. Depending on how the pressure zone is created in your Surface-water Modeling System (SMS) project, this can be a tricky process for SRH-2D to handle. Here are some steps and tips for creating this feature successfully in SMS.

1 Use Quadrilateral Elements

Create quadrilateral elements between the boundaries of the pressure zone. Using quadrilateral elements tends to increase the stability and reliability of the SRH-2D model run. Quadrilateral elements can be created in one of two ways.

The first is to create the quadrilateral elements when creating the 2D mesh. Create a polygon for the area between and around the pressure zone. Assign this polygon with the Patch mesh type in the 2D Mesh Polygon Properties dialog.

The second method is to create the quadrilateral elements directly in the mesh using the Split/Merge tool and the Switch Element tool. This can be time-consuming, so it is only recommended for small adjustments.

Box culvert example
2 Create Voids

Create voids in the mesh on either side of the pressure zone. There are two options for creating these voids, but one option seems to work better.

The first option, and the more stable one, is to create the voids on either side of the pressure zone when generating the mesh. Create the voids as polygons and assign them the None mesh type. It is generally best to make each void a quadrilateral polygon to imitate the thickness of a concrete wall or barrier.

The second option is to generate the mesh then use the Select Elements tool to select and delete the elements where the voids should be. Using this method requires renumbering the mesh nodes. There is a risk that you will not be able to delete all of the nodes related to the elements which can make your mesh unusable to SRH-2D.

3 Assign Boundary Conditions

Two arcs are needed to define the pressure zone. Each arc should be created on an SRH-2D boundary condition coverage. When creating the arcs, make certain all 2D mesh elements between the arcs are quadrilateral elements. Also, it is advisable to have at least one row of quadrilateral elements just past the downstream arc.

Once the arcs have been drawn, select both arcs and open the SRH-2D Linear BC dialog. Set both arcs to the Pressure type, making sure the correct arc ID is assigned to upstream versus downstream, and turn on the Overtopping option.

Both the boundary condition coverage and the 2D mesh can be added to your SRH-2D simulation to have a pressure zone with overtopping included in the results.

Try out adding a pressure zone in SMS today!

This post was originally published September 12, 2018.

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Build Watershed and Streams from Raster Data

Delineating a watershed area into a usable model can be a daunting process. Two new tools in the Surface-water Modeling System (SMS) Toolbox make defining a watershed domain quick and easy. Introducing the Streams from Rasters and the Watershed from Rasters tools.

These two tools are found in the Coverages folder in the Toolbox.These two tools can extract data from an imported raster to automatically generate the feature objects for watershed streams and domains for your SMS model.

The first tool, Streams from Raster, will evaluate the raster elevation data, extract the direction of runoff, create connected arcs, and put it into a separate coverage for you. You’ll need a directional raster in order to run the tool.

The Streams from Raster tool will show the entire runoff flow based on elevation in the selected raster. If water starts here, then it will go in that direction until it ends up there in that stream bed. You can see and trace the most likely paths for water flow until it hits the lowest point possible for that flow path. This can help you plan where to place your stream arcs for your model.

A watershed domain created from raster data

The Watershed from Rasters tool creates a domain of the watershed area. This tool uses an amalgamation of several processes that operate in a particular order in the background as the tool runs. Several of these processes have been added to the Toolbox, including Streams from Raster, to run as separate tools, if desired. Once run, you will end up adding feature objects that define a domain to a coverage.

Then, the feature objects can be used to create a geometry (2D or 3D meshes or UGrids, etc.) of the watershed area. By using the Watershed from Raster tool, it enhances the speed at which a model can be created.

Head on over to SMS and try delineating a watershed with these new tools in your next model.

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Utilizing Contour Legends

The Groundwater Modeling System (GMS) contains many tools for visualizing data. The contour visualization tools are particularly helpful in viewing solution data. With contours, GMS provides several options for how contours will be displayed, including options for the contour legend. When a legend is added to the contour display, it is not always clear what the units of the values shown in the legend are. With GMS 10.8 improvement to the Contour Legend Options allow displaying the data units with the legend.

The Contour Legend Options dialog is available for the contour dataset displayed in the Graphics Window. Accessed from the Legend Options button on the Contour Options dialog, the Contour Legend Options dialog controls the formatting and location of a displayed legend. The tool is only available if the Legend check box on the Contour Display Options Dialog is checked. This dialog includes formatting options such as a title field, a font selection button, as well as fields for height and width. Furthermore, the dialog offers location options that includes a combo box for specifying the location of the displayed legend. Visit our wiki page to view descriptions of each feature this dialog provides.

Here is a step-by-step of how to execute this feature:

  1. Select Contour Options.
  2. At the bottom of the Dataset Contour Options dialog, ensure that the Legend option is checked.
  3. Select Options in the Legend section.
  4. In the Formatting Section of the Contour Legend Options dialog, enter the respective unit keyword: "UNITS" for DS (Datasets) and "TUNITS" for (Time steps).
Contour legend options in GMS

The ability to add the unit type to the legend is a user requested feature that helps make presenting data clearer for your audience. This and other improvements are continuously being added to GMS. Head over to GMS and check out the options for legend displays and other features.

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Tips for Manually Editing Stream Arcs

Did you generate stream arcs in your Watershed Modeling System (WMS) model that you discovered later needed to be adjusted? Or maybe the outlet point’s position needs to be slightly adjusted. You can manually edit streams without using any of the wizards available in WMS, but you do need to be careful. Here are some tips on how to do it and what to watch for.

To manually edit your stream arcs, you will need to use the tools in the Map module. You can select and move a stream node or vertex to alter the path of a stream. You can also change a node to a vertex, create new feature points where needed, and manually edit properties in the Properties screen. You may wish to change your Display Options so that you can see the stream arcs, and vertices more clearly. Used carefully, you can make minor adjustments without using the wizards.

If you need to shift a stream outlet point or other major node, you can use the Select Feature Point/Node tool to select the stream outlet point and drag it to a new position. When the stream outlet point is originally on an arc but then moved away from the arc, the arc can snap to the new outlet location. Be careful where you move your stream outlet point, (or any stream arc vertex), especially if you accidentally shift it to a higher elevation, as this can create digital dams or break the model.

Streams in WMS

If you have extremely long stream arcs, or need to make precise corrections around obstacles, land formations, or buildings, you can manually add one or more vertices to the arc using the Create Feature Vertex tool. Then, you can then use the Select Feature Vertex tool to select and move them to better locations within the bounds of the model. This can be especially useful if you discover that one or more of your steam arcs now cross outside the bounds of the delineation arcs after manually editing them.

If you’ve changed a stream arc by adding vertices or just moving locations, you’ve also changed the vertex distribution along the arc. It may be necessary to redistribute the vertices again.

You will want to check elevation values against the DEM. If you have moved a stream arc point, you may have shifted it from its elevation. You may need to re-interpolate elevations back onto the stream arcs.

It is also recommended that manual edits be done prior to defining the model, otherwise you may discover that making these edits, while improving the stream arcs, has broken the model. If that happens, you may need to re-delineate the watershed. You can go back to the wizard that you used to delineate your watershed model and skip to the appropriate step to rework your model from there.

This manual editing of stream arcs is different from the GSSHA’s Smooth Stream/Pipe Arcs tool and works outside of any wizards within WMS.

Try out any of the tips with your watershed projects in WMS today!

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2D Mesh Editing Versus Regeneration: Which is More Apt?

If you need to make a change to a mesh, should you use the toold in the 2D Mesh module to edit, or instead regenerate the mesh? A 2D mesh consists of elements that define the computational domain of the numerical model. A numerical simulation requires a geometric definition of its domain– the mesh, available for use in SMS 13.3. Occasionally when constructing a mesh, a moment occurs where the mesh is insufficient for any reason.

In most cases the recommendation is to regenerate the mesh; as opposed to editing the mesh manually. The following list involves common circumstances where one may manually edit a mesh:

  • There is no mesh generator coverage present.
  • Deleting Outer Elements: Since the triangulation process creates elements (i.e. thin triangles) outside the mesh boundaries, deleting outer elements provides some refinement.
  • Merging Triangles/Element: Numeric solvers are more stable and accurate when quadrilateral elements are rectangular and triangular elements are equilateral.
  • Editing Individual Elements: After compound edits, a mesh could benefit from individual manipulation to increase stability. Swapping edges: Think of the two triangles as a quadrilateral, and the common edge between them is a diagonal of the quadrilateral. By swapping this common edge, it changes to be along the opposite diagonal of the quadrilateral. If this edge is clicked again, it returns back to its original state.
  • Turning a specific element into a void element.

You may make edits in the Mesh Generator coverage. Manual edits should be intentional and reserved for small sections of a mesh. Generally, manual edits of a mesh ought to be minimal.

In nearly all cases the recommendation is to regenerate the mesh; as opposed to editing the mesh manually. This is because any process that edits a mesh, causes the node and element ordering to become disorganized. Additionally, editing a mesh invalidates any solution files that have been previously saved. Manually editing a 2D mesh risks creating issues with the assigned elevation data or other datasets being used. As such, if there is a solution dataset attached to the mesh, the model simulation should be re-run.

Example of file generated mesh preview

A useful tip is reviewing your mesh before generating, using the preview tools that are available in a given dialog. Make adjustments to the arcs, vertices, and polygons on the mesh. Do not be afraid to add more arcs, vertices, or polygons if further refinement is needed.

If you want to generate a new mesh with the desired edits, you will need to create a mesh generator coverage. The following are examples of tools that can create a new mesh:

  • Map → 2D Mesh tool.
  • 2D Mesh from 2D Grid in the toolbox.
  • Additionally, most of the Unstructured Grid tools may be utilized to generate a new mesh.

Make use of the mesh editing and generating capabilities of SMS 13.3 today!

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Export UGrids Seamlessly With the Export UGrid Tool

Do you have an unstructured grid (UGrid) in the Groundwater Modeling System that you want to share with other projects or applications? Having a portable UGrid allows you to share data between projects or with colleagues. The Groundwater Modeling System (GMS) has several ways to export data, including UGrids, from a model. The Export UGrid tool in the Toolbox allows you to export your UGrid to a file location your computer.

When you open the Export UGrid tool, found under the Unstructured Grids section in the Toolbox, you have only three steps to take:

  1. Select the UGrid you wish to export.
  2. Select the file type.
  3. Save it with a name and location.

There are three primary file types in the Export UGrid tool to choose from: XMC, STL, and OBJ. Two of these, XMC and STL, have two additional variations on the formats for saving: ASCII and binary.

Example of file generated with the Export UGrid tool

Aquaveo has provided the XMC format, our format, for exporting structured and unstructured grids of all varieties: 2D grids, 3D grids, quadtree/octree, nested, and voronoi.

GMS also provides the STL file format. This stereolithography file can be used with 3D CAD printing and should be able to be read by CAD software. It may also be converted to other file formats. This can only be used with triangular grids.

The last format type is OBJ. A geometry definition file format originally created for animation software, it has since been used for modeling and simulations in various applications. An OBJ file can be converted to STL and other formats. The OBJ format is limited to triangular grids only.

The ASCII formats of both the XMC and the STL file types, as well as the OBJ file type can be viewed and edited in a text editor.

The variety of file formats gives you flexibility in choosing how best to use the data. Head on over to GMS and see what the Export UGrid tool can do for you.

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Discover the Refine UGrid Tools in SMS

The Surface-water Modeling System (SMS) continues to expand its capabilities. Currently, SMS is expanding to make more use of unstructured grids. An unstructured grid (UGrid) is a flexible geometric object that can include cells such as 2D and 3D cells with any number of faces and nodes. This flexibility allows for more realistic modeling of geological features.

In SMS, UGrids can be imported directly or created by converting an existing geometry such as a 2D mesh, 2D scatter set, Quadtree or map feature objects. When creating an UGrid from an existing geometry, it is usually best to make certain the geometry already refined to the level you need for your project. However, sometimes the Ugrid needs to be refined after it has been generated or imported. To do this, SMS provides two tools for refining UGrids: Refine UGrid and Refine UGrid by Error.

Both tools are located in the SMS Toolbox under the Unstructured Grids folder.

The Refine Ugrid uses an existing UGrid then splits (refines) the elements into smaller elements. The Refine UGrid tool provides you with the option to select datasets with “locked” nodes—any node with a non-zero scalar value. Any cell edges that contain one or more locked nodes will not be split. Utilizing such a tool will equip you to complete a surface-water modeling project with focused accuracy and efficiency. .

Example of refining a UGrid

Similar to the Refine UGrid tool, the Refine UGrid by Error tool produces a 2D UGrid that has been refined as a result of an existing 2D UGrid, however this tool integrates elevation rasters into the process. Entering a value that guides the acceptable error threshold, the maximum number of iterations to perform, and the necessary elevation rasters are all required components of the input parameters for this tool.

Being able to refine UGrids adds increased accuracy for your surface-water projects in SMS. Check out the refine UGrid tools in SMS today!

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Eliminate Null Values in SMS

Does your Surface-water Modeling System (SMS) model contain null values? Null values can be useful at times. Some models are even built around them. But what about when you don’t want them in your model? The tools in the Toolbox have ways to change, correct, or exclude data, including null values, without needing to manually edit the files and re-importing them, to clean up the data. These tools have multiple uses for viewing data in different ways, modifying current datasets, and creating new ones from the modifications made.

The Toolbox holds a very useful option in the Filter Dataset. It can be used to modify data in existing datasets by using various filters to include, exclude, or change the data being processed. When you have null values inside your project that you wish to exclude, you can use this tool to eliminate null values and assigning them to 0.

In order to use the Filter option, follow these steps:

  1. Go to Toolbox | Dataset | Filter Dataset.
  2. Click on Run Tool…
  3. Under Input dataset, select the dataset from the dropdown.
  4. For the If condition, select null from the dropdown.
  5. For Assign on true, select Specify from the dropdown.
  6. Enter 0.0 for the Specified Value.
  7. Under Output dataset, enter a new name for the results of the test.
  8. Click OK to run the tool.
Example of the Filter Dataset tool

Once you have created a filtered dataset, the new dataset can then be viewed in the simulation or used with other tools in the toolbox to modify, view, or create other new datasets for better visualization.

This filter function can also be found under Data | Data Set Toolbox… under the Tools section in the left-hand column. It has a slightly different look but the exact same utility.

Head over to SMS and try out the Filter tool to see how it can improve your model results and data visualizations.

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Streamlining GMS by Using Keyboard Shortcuts

No matter how long you have been using the Ground-water Modeling System (GMS), you can enhance your experience with keyboard shortcuts. GMS comes equipped with various keyboard shortcuts–quick keys, hotkeys, accelerator keys, keybindings–in order to make the process more efficient for you. Whether you are just beginning or seasoned, such shortcuts are useful for any water modeling project.

The newest addition to the collection is related to the GMS unstructured grid (UGrid) feature, and facilitates progress with one click: Select all cells in UGrid layer using the “l” (L) key.

New select UGrid layer shortcut

Here are a few more shortcut options that expedite the groundwater modeling process:

  • CTRL+D (Display Options): Quickly populate your display options module for view and modification.
  • CTRL+F (Frame Image): Use this option to scale and frame your model in the Main Graphics Window.
  • View: Utilize these options and view your project from any perspective quickly.
    • Shift+P (Plan View)
    • Shift+F (Front View)
    • Shift+S (Side View)
    • Shift+O (Oblique View)

With all of the intricacies of the GMS software, simplifying even the smallest commands may increase productivity in infrastructure planning:

  • CTRL+N (New Project): Clear the contents of your previous project easily with this command.
  • CTRL+O (Open File): Import a new file with this command.
  • Delete Key: Delete objects easily with this command.
  • CTRL+A (Select All): Select all objects easily with this command.
  • CTRL+U (Unselect All): Unselect all objects easily with this command.

Mastering keyboard shortcuts is a key aspect of becoming a proficient user of GMS. By taking advantage of these time-saving tools, users can navigate the environmental engineering software more efficiently, focus on their modeling tasks, and ultimately achieve better results in their water modeling projects. Use the "GMS Keyboard Shortcuts" article on the Aquaveo wiki to view these commands and more.

Additional shortcuts continue to be added to GMS. Access the latest version of GMS to make use of the newest shortcuts today!

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